p.s. and how did you create the .mnc in the first place? The safest thing
by far is to go right from the dicoms. Does the .mnc show up properly in
tkmedit and/or scuba?
On Fri, 28 Sep 2007, Doug Greve wrote:
How do they look in tkmedit? How do you know the problem is not in neurolens?
What do you get if you run mri_info on those volumes? Is it consistent and
accurate?
doug
roberto toro wrote:
(sorry. I just clicked reply, and didn't send the screenshots to the
list)
You can see in the images (I'm using neurolens) the contraction of the
left-right axis and the shift: the black space at the left and right
sides is even originally but uneven in the converted data. In another
slice (not included) you can see a little bit of the right ear
appearing from the left side.
There's also the problem with the rotation, the nose is originally
pointing to the right but then it's pointing down, which is why the
axial slices look coronal and vice-versa. Keeping that in mind, you
can see that left and right hemispheres are swapped (look at the shape
of the posterior horn of the ventricles, which is longer in the left
hemisphere)
thanks,
roberto
---------- Forwarded message ----------
From: roberto toro <[EMAIL PROTECTED]>
Date: Sep 27, 2007 4:23 PM
Subject: Re: [Freesurfer] convert mnc->analyze->mgz
To: Bruce Fischl <[EMAIL PROTECTED]>
On 9/27/07, Bruce Fischl <[EMAIL PROTECTED]> wrote:
Hi Roberto,
can you send us the command line and full screen output of the minc to
mgz step? It shouldn't change the aspect ratio.
thanks,
Bruce
hi Bruce,
here's the command:
roberto% mri_convert P.mnc P.mgz
mri_convert P.mnc P.mgz
reading from P.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to P.mgz...
roberto%
and I attach screenshots of the result (which is scaled and shifted).
thank you,
roberto
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